Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• )cyanophenylacetonitrile) fluorophores for easy access, which will contribute to the rapid dissemination of the RNA imaging approaches associated therewith. Keywords: covalent RNA labeling; FLAP; fluorophore synthesis; HBC530; self-alkylating ribozymes; Introduction The discovery of fluorescent reporters, such as green

• , however, there was no complementary RNA-based tool with comparable live-cell-imaging properties. Based on the autocatalytically generated fluorophore 4-(p-hydroxybenzylidene)imidazolidin-5-one (HBI) in GFP, in vitro selection on derivatives of HBI led to the discovery of the first fluorogen-activating

• are non-covalently bound to their fluorophore and despite high (usually nanomolar) binding affinities this can pose problems for RNA live-cell imaging. For instance, diffusion of the ligand and non-specific binding lead to unfavorable background and/or signal loss [10]. To address these problems, our

Germanyl triazoles as a platform for CuAAC diversification and chemoselective orthogonal cross-coupling

• John M. Halford-McGuff,
• Thomas M. Richardson,
• Aidan P. McKay,
• Frederik Peschke,
• Glenn A. Burley and
• Allan J. B. Watson

Beilstein J. Org. Chem. 2024, 20, 3198–3204, doi:10.3762/bjoc.20.265

• the CuAAC process to more challenging substrates. Using fluorophore- and cholesterol-derived azides, coupling with the triethylgermanyl alkyne delivered the expected products 26 and 27, respectively, in good yield, enabling possible downstream diversification of these functional molecules of relevance

Photoluminescence color-tuning with polymer-dispersed fluorescent films containing two fluorinated diphenylacetylene-type fluorophores

• Kazuki Kobayashi,
• Shigeyuki Yamada,
• Motohiro Yasui and
• Tsutomu Konno

Beilstein J. Org. Chem. 2024, 20, 2682–2690, doi:10.3762/bjoc.20.225

• fluorophore 1a and green–yellow fluorophore 1c PMMA dispersion films containing 1 wt % of blue fluorophore 1a and green–yellow fluorophore 1c in various weight ratios were prepared. Their PL spectra and photophysical data are depicted in Figure 4 and Table 2 summarizes the collected photophysical data. As

• mentioned above, the PMMA film containing 1 wt % of fluorophore 1a with a methoxy group exhibited a single PL band with a λPL at approximately 415 nm and dark blue PL with chromaticity coordinates of (0.16, 0.09). In contrast, the PMMA film containing 1 wt % of fluorophore 1c with a diphenylamino group

• showed green–yellow PL with a λPL at approximately 506 nm and chromaticity coordinates of (0.28, 0.60). The PL behavior of the 1 wt % PMMA film blended with blue fluorophore 1a and green–yellow fluorophore 1c in a 50:50 ratio was evaluated, and two PL bands appeared, namely major and minor PL bands with

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• -PAGE) and visualized by in-gel fluorescence scanning (Figure 6A). In this approach the tag is a suitable fluorophore. Previously, during an introduction period of a chemical proteomics workflow of activity-based protein profiling (ABPP), the resulting fluorescent bands might be simply cut out from the

• fluorophore for in-gel analysis, a terminal azide for CuAAC to label probe–protein conjugates, and a trypsin-cleavage site, which allows to release the modified probe–peptide conjugates together with other unmodified tryptic peptides from the streptavidin beads (Figure 14). In principle, the release of

• ) Comparison of DDA and DIA techniques. B) Diagnostic ions mining. C) Open search. D) Closed search. In-gel analysis using a tag with fluorophore (A) or via shift-assay (B). Reporter linkers. A) DMP-tag. B) AzidoTMT tag. C) SOX-tag. D) Imidazolium tag. *A star indicates the possible introduction of stable

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• to the presence of competitive processes, such as energy or electron transfer. Trolez et al. investigated the photoluminescence properties of various fluorophore-containing TCBDs synthesized via reactions between ynamides and TCNE [139]. The study revealed that numerous fluorenyl derivatives and

Synthesis of N-acyl carbazoles, phenoxazines and acridines from cyclic diaryliodonium salts

• Nils Clamor,
• Mattis Damrath,
• Thomas J. Kuczmera,
• Daniel Duvinage and
• Boris J. Nachtsheim

Beilstein J. Org. Chem. 2024, 20, 12–16, doi:10.3762/bjoc.20.2

• possible products. We obtained p-halogenide- and p-pseudohalogenide-substituted compounds 2c–g in good yields of 76–87%. It is noteworthy that the para-chloro-substituted compound 2f is a known fluorophore [5]. The reaction tolerated methoxy- and methyl ester-substitution to give 2h and 2i in 84% and 90

Biphenylene-containing polycyclic conjugated compounds

• Cagatay Dengiz

Beilstein J. Org. Chem. 2023, 19, 1895–1911, doi:10.3762/bjoc.19.141

• . When the fluorescence properties of compounds 62, 63, and 64 were examined, it was observed that compound 62 exhibited strong fluorescence, making it an excellent fluorophore (λmax,em = 508 nm, Φem = 0.58) . On the other hand, compound 63 showed weaker fluorescence compared to 62 (λmax,em = 666 nm, Φem

Thienothiophene-based organic light-emitting diode: synthesis, photophysical properties and application

• Recep Isci and
• Turan Ozturk

Beilstein J. Org. Chem. 2023, 19, 1849–1857, doi:10.3762/bjoc.19.137

• pull–push fluorophore, DMB-TT-TPA (8), having TPA and DMB units as donor and acceptor units that were linked through a 4-MeOPh-substituted TT core as a π-spacer. The photophysical properties of the fluorophore were investigated by spectroscopic methods. Moreover, DMB-TT-TPA (8) was fabricated as an

• current efficiency of 10.6 cd/A, and maximum power efficiency of 6.70 lm/W. Results and Discussion Design and synthesis The OLED fluorophore, DMB-TT-TPA (8, Scheme 1), having a donor–π–acceptor (D–π–A) system, was synthesized according to our previously reported methods [20][21][22][23][36][38]. The

• 4-bromo-N,N-diphenylaniline (5) with n-butyllithium at −78 °C and addition of 2-isopropoxy-4,4,5,5-tetramethyl-1,3,2-dioxaborolane. The Suzuki-coupling reaction of TT 4 with borolane 6 produced the intermediate 7 in 81% yield. The target D–π–A-type fluorophore, DMB-TT-TPA (8), was produced by

A deep-red fluorophore based on naphthothiadiazole as emitter with hybridized local and charge transfer and ambipolar transporting properties for electroluminescent devices

• Suangsiri Arunlimsawat,
• Patteera Funchien,
• Pongsakorn Chasing,
• Atthapon Saenubol,
• Taweesak Sudyoadsuk and
• Vinich Promarak

Beilstein J. Org. Chem. 2023, 19, 1664–1676, doi:10.3762/bjoc.19.122

• Frontier Research Center, Vidyasirimedhi Institute of Science and Technology, Wangchan, Rayong 21210, Thailand 10.3762/bjoc.19.122 Abstract Herein, we report the synthesis and characterization of an efficient ambipolar charge-carrier-transporting deep-red fluorophore (TPECNz) based on a donor–acceptor

• –donor (D–A–D)-type molecule and its application as a non-doped emitter in an organic light-emitting diode (OLED). The fluorophore TPECNz contains naphtho[2,3-c][1,2,5]thiadiazole (Nz) as a strong acceptor unit symmetrically functionalized with N-(4-(1,2,2-triphenylvinyl)phenyl)carbazole as a donor and

• coordinates of (0.664, 0.335)), an EQEmax of 3.32% and exciton utilization efficiency (EUE) of 47%. Keywords: ambipolar material; deep red fluorophore; hybridized local and charge transfer; naphthothiadiazole; OLED; organic light-emitting diode; Introduction Recently, organic fluorophores with efficient

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• revealed a distorted ruffled molecule with a macrocycle incorporating a pyrroloindole subunit formed through the fusion between the para-phenylene ring and the pyrrolic nitrogen. 42 demonstrated fluorophore behaviour with relatively large fluorescence quantum yields of 10–20% and singlet state lifetimes of

Cyclodextrins permeabilize DPPC liposome membranes: a focus on cholesterol content, cyclodextrin type, and concentration

• Ghenwa Nasr,
• Hélène Greige-Gerges,
• Sophie Fourmentin,
• Abdelhamid Elaissari and
• Nathalie Khreich

Beilstein J. Org. Chem. 2023, 19, 1570–1579, doi:10.3762/bjoc.19.115

• work was to reveal how CHOL would modulate the CDs effect on the membrane. Hence, liposomes made of dipalmitoyl phosphatidylcholine (DPPC) and various CHOL contents (DPPC/CHOL 100:10, 100:25, 100:50, and 100:100) encapsulating the hydrophilic fluorophore, sulforhodamine B (SRB), were prepared and

• of substitution are represented in Figure 2. The effect of the CDs on the membrane permeability was monitored by following the release of a hydrophilic fluorophore, sulforhodamine B (SRB), from liposomes composed of DPPC and different CHOL content upon exposure to different concentrations of CDs. To

• carried out on a spectrophotometer (Hitashi F-7000 Spectrofluorometer) at an excitation wavelength of 535 nm and an emission wavelength of 590 nm. The emission spectrum was recorded in the range 540–700 nm. The results of the permeability study were expressed as the percentage of the fluorophore released

N-Sulfenylsuccinimide/phthalimide: an alternative sulfenylating reagent in organic transformations

• Fatemeh Doraghi,
• Seyedeh Pegah Aledavoud,
• Mehdi Ghanbarlou,
• Bagher Larijani and
• Mohammad Mahdavi

Beilstein J. Org. Chem. 2023, 19, 1471–1502, doi:10.3762/bjoc.19.106

• pyrrolines 62 were obtained by changing the reaction solvent to MeCN. Also, organic fluorophore compounds such as benzothienopyrrole and bis-thiolated boron dipyrromethene can be achieved from 3-thiolated pyrroles. Mechanistic studies showed that the oxidative species HNO and HCHO were generated through a

pH-Responsive fluorescent supramolecular nanoparticles based on tetraphenylethylene-labelled chitosan and a six-fold carboxylated tribenzotriquinacene

• Nan Yang,
• Yi-Yan Zhu,
• Wei-Xiu Lin,
• Yi-Long Lu and
• Wen-Rong Xu

Beilstein J. Org. Chem. 2023, 19, 635–645, doi:10.3762/bjoc.19.45

• display distinct peaks at δ 7.50–6.70 in their 1H NMR spectra (Figure 1) and at δ 145–120 ppm in their 13C NMR spectra (Figure S1 in Supporting Information File 1), corresponding to the proton resonances of the benzene rings and the carbon resonances of the whole fluorophore, respectively. The appearance

Functionalization of imidazole N-oxide: a recent discovery in organic transformations

• Koustav Singha,
• Imran Habib and
• Mossaraf Hossain

Beilstein J. Org. Chem. 2022, 18, 1575–1588, doi:10.3762/bjoc.18.168

• perfluoroaryl-substituted 2H-imidazole products, a push–pull fluorophore system was discovered, which can be useful for the preparation of fluorometric sensor materials because of the solvent-dependent intramolecular charge transfer effect (ICT). Here, two reaction pathways were designed: (A) addition

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• tetraphenylethene (TPE) units which act as an aggregation-induced emissive (AIE) fluorophore [65]. The newly designed TPE-based tetraimidazole donor 19 has been treated with 180°/120° trans-Pt(II) acceptors which led to the coordination-driven self-assembly of 3D discrete molecular cages in aqueous medium (Figure 5

Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase

• Peterson de Andrade,
• Sanaz Ahmadipour and
• Robert A. Field

Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24

• both enzymes (Figure 3A) (and TcTS transferase activity in the presence of an acceptor substrate, such as lactose – Figure 3B) by releasing the fluorophore 4-methylumbelliferone (MU) for detection upon cleavage of the substrate 2'-(4-methylumbelliferyl) α-ᴅ-N-acetylneuraminic acid (MUNANA). Compounds

Synthesis and bioactivity of pyrrole-conjugated phosphopeptides

• Qiuxin Zhang,
• Weiyi Tan and
• Bing Xu

Beilstein J. Org. Chem. 2022, 18, 159–166, doi:10.3762/bjoc.18.17

• the designed peptides combines solution synthesis of the enzyme trigger or the fluorophore with the solid-phase synthesis of the pyrrole-peptide conjugates. We used phosphorus pentoxide and phosphoric acid to react with ᴅ-tyrosine, ʟ-tyrosine, ʟ-serine, or ᴅ-serine to produce ᴅ-phosphotyrosine, ʟ

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Circularly polarized luminescent systems fabricated by Tröger's base derivatives through two different strategies

• Cheng Qian,
• Yuan Chen,
• Qian Zhao,
• Ming Cheng,
• Chen Lin,
• Juli Jiang and
• Leyong Wang

Beilstein J. Org. Chem. 2021, 17, 52–57, doi:10.3762/bjoc.17.6

• -TBPP and S2N-TBPP are +0.0021, and −0.0025, repectively (Figure 1b), which is larger than many small organic molecules [25]. In order to avoid a tedious chiral separation of rac-TBPP, we tried to construct the CPL-active material by co-assembling the achiral fluorophore rac-TBPP with a chiral gelator

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• organic fluorophore (reporter) with a specific peptide sequence is the common approach for designing peptide-based fluorescent probes [16]. Fluorophores on peptidic arms perform as reporter during the interaction with biomolecules [17][18]. The interaction with biomolecules will alter the fluorescence

• ] formation have been frequently adopted. Several classes of environment-sensitive fluorophores are currently available and heavily used by the biological community. Upon interaction with a biomolecule, the fluorophore induces a change in the spectral properties. The fluorescence intensity is generally

• enhanced and blue-shifts after affinity/recognition in a polar solvent. Several computational studies confirmed that the spectral change is caused by the insertion of the environment-sensitive fluorophore in the hydrophobic domains/grooves of the target protein/DNA (Figure 1A). The major problem of these

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

• Marius H. Heddinga and
• Jens Müller

Beilstein J. Org. Chem. 2020, 16, 2870–2879, doi:10.3762/bjoc.16.236

• applied in combination with a fluorophore (fluorescein), a quencher (DABCYL), and complementary oligonucleotides to devise a system referred to as structure-switching signaling aptamer [40]. Based on this concept, two systems were devised to investigate whether the Im–Ag(I)–Im base pairs could be applied

• additional bases of 1q2 should be able to form two more canonical base pairs with the aptamer and therefore compensate for the destabilization caused by the imidazole mismatches. As expected, all fluorophore-labeled aptamers show a more effective quenching upon the addition of 1q2 (Figure S5 in Supporting

• . Surprisingly, the affinity of 1b remains almost unchanged. Overall, it seems that the fluorescein label influences the affinity of the aptamers to ATP only in the case of 1b/1bf where the imidazole moiety is located closest to the fluorophore. Conclusion The metal-mediated Im–Ag(I)–Im base pair can be used to

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• microarray scanner (for example, Genepix 4400A). Microarray scanners are fluorescence scanners which utilize laser technology, such that the excitation wavelength is generated by specific lasers. Commonly used laser wavelengths are 488 nm, 532 nm, 594 nm and 635 nm, which match with usual fluorophore labels

• on detecting reagents (e.g., labeled GBP, antibody or streptavidin). The emission wavelength of the fluorophore determines the filter used by the scanner before the intensities are measured by a photomultiplier tube (PMT) or by CCD camera. Currently, CCD camera systems are less sensitive as compared

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA. Keywords: amino acid–fluorophore conjugate; circular dichroism; DNA/RNA recognition; fluorescence; intercalation; naphthalene diimide

• developed several series of fluorophore–amino acid conjugates, thereby making use of the availability of C- and N-terminal amino acid residues for peptide-bond formation. Also, several short multichromophoric peptide constructs were prepared and studied with regard to their interactions with DNA/RNA [11][12

• preparing novel fluorophore–amino acid (AA) conjugates. The amino acids (S)-2,3-diaminopropionic acid (ʟ-Dap) and (S)-2,6-diaminohexanoic acid (ʟ-Lys) were chosen to test the difference in the aliphatic linker lengths (Figure 1) on DNA/RNA binding. For comparison purposes, reference compound 5 with 2

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• )-labeled analog MPC-2 carries an additional dodecanyl linker between the citronellyl unit and the fluorophore. This is intended to increase the hydrophobic interactions between the probe and the lipid bilayer and also to increase the flexibility. More specifically, the probe should adopt a U-shaped

• structure in which the citronellyl–dodecanyl linker is located in the phospholipid membrane, and the mannose and the NBD are positioned in the surrounding aqueous medium. The close proximity of the NBD fluorophore to the membrane–water interface [30][31] allows for fluorescence-based scramblase assays

• wherein the NBD can be detected with dithionite. The latter reduces the nitro group of the NBD rapidly into an amino group, rendering the fluorophore nonfluorescent [32][33][34]. While there are no noteworthy difficulties in the synthesis of the molecular probe MPC-1 to report, the same cannot be said for

Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles

• Kazuyuki Sato,
• Akira Kawasaki,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2020, 16, 1411–1417, doi:10.3762/bjoc.16.117

• -opening reaction of 4-fluoroisoxazoles and exhibited highly fluorescent luminescence and aggregation-induced emission (AIE), showing promise as a new fluorophore. Keywords: aggregation-induced emission; boron ketoiminates; fluorescent probe; α-fluorinated boron ketoiminates; 4-fluoroisoxazoles

• suggesting that they might have the potential to act as a fluorophore [33]. During the synthesis of 3,5-diaryl 4-fluoroisoxazoles 3 according to the previous method (Scheme 2), we noted that 3,5-bis(4-methoxyphenyl)-4-fluoroisoxazole (3b) and 3,5-bis(4-trifluoromethylphenyl)-4-fluoroisoxazole (3c) exhibited